Life in the Flames
by Angnix
Summary: Sonic 06 Based. The Flames have been released into the world. What is life like now for the remaining heroes one year afterwards? ShadowxRouge Tragedy. Story Complete!
1. Chapter 1: The Flames are Released

Life in the Flames

By Angnix

PG-13

A new Sonic 06 based fic, about life after Iblis was released and it's a Shadow and Rouge story. Enjoy!

Chapter 1: The Flames are Released

_The sky over Kingdom Valley was covered end-to-end with a thick blanket of foreboding gray clouds. Sonic could see the red and black Egg Carrier in the distance. A Sonic Boom emanated from the Blue Hedgehog as he broke the speed of sound, trying to save Princess Elise who was trapped on board. The ship sprouted three long plumbs of flames. Sonic ran even faster, he knew this didn't look good. What happened next would be forever burned into Sonic's brain. The ship with the most sickening crunching sound he ever heard plowed into a distant mountain. The orange light that came from the ship almost burned Sonic's eyes, but emotionally instead of physically. In despair, he sank to his knees. But Silver and Blaze were not there close behind him. This was before the Time Paradox that eventually lead to Sonic saving Elise by traveling back through time itself. There was no way he could save her. It was too late. Cautiously, Sonic went up to the crash sight, to see if anything made it out alive. Suddenly, a small ship arose out of the Egg Carrier's ashes. Sonic always wondered how Eggman always survived major explosions the way he did. Sonic was about to go after him, maybe he had Elise with him! But, he stopped in his tracks when he saw a single feather sticking out from under a piece of burning wreckage. Sonic cautiously walked over and lifted up the jagged piece-of-metal. What was underneath is to horrible for me to describe. Suddenly, a small ball of Flame arose from Elise's body. Sonic was taken aback, was even her soul set on fire by the burning wreckage and was trying to escape? Eggman with a very twisted look of happiness exclaimed "So killing her was the secret to releasing the Flames! Now all I have to do is figure out how to catch it!" Sonic didn't say a word or even move. How could Eggman do something as cruel as letting her die? The Flame went to the North, while Eggman went the opposite direction. Sonic decided to follow Eggman, he couldn't get away with this! In the distance, a member of the Soleanna Guard who was also tracking Elise caught a glimpse of Sonic speeding away from the wreckage. But the Guard saw him incorrectly and even used a cell phone to tape him through the thick smoke and thought GUN Agent Shadow caused the wreck that killed Elise… _

A year had passed since that day. Eggman is still trying to capture that Flame, but it seems to elude every single plan he has come up with. Sonic and friends are trying to stop the Flame. The Flame started to find the long missing "Mysterious Stones of Soleanna" which Tails quickly determined were one and the same as the Sol Emeralds they had encountered before. This of course confused Tails, didn't they go back to the alternate dimension and why didn't he realize their existence in his world before? But it did not matter, every Sol Emerald Iblis, the Flames of Disaster found meant the death of millions more people as it changed into more powerful forms. Of course they tried to evacuate people, but it's hard to evacuate large areas of land. Plus the environmental damage all the smoke caused to the atmosphere caused millions more to starve to death, even if they did not live within the Flame's reach. Everyone was afraid the Flames would cover the entire planet when it found all 7 Sol Emeralds. And the Chaos Emeralds… where did they go? Those Flames… Sonic felt so responsible. He even tried to tell people it was his fault, he should be punished. But nobody would listen to Sonic, they wanted their Blue Hero to stop the Flames. Those Flames seemed hungry for living things. Eventually they consumed Tails and Knuckles, even Cream and her Mother. If only the Chaos Emeralds could be found so those Flames could be stopped! Meanwhile, Shadow was blamed with the Princess's death and that was eventually stretched to include releasing the Flames, even though he too is trying to stop the Flames…

"Hmph, don't you realize that I am trying to help you?" said a very tired Shadow after defeating a whole battery of GUN Laser Hunters in the middle of Crisis City. This place was so chocked in smoke, night was ink black except the orange glow of the lava, and the daytime was an orange haze. Now it's Midnight and the orange glow shown brighter than before. The Flames were getting higher on the buildings, as if they were going after Shadow themselves. Crisis City used to be downtown New City Soleanna, but was now where the creature's power was felt most. An agent that once worked by Shadow's side all the time now had a gun pointed to his head.

"Say that all you want, but we know what kind of Princess Killing and Iblis-releasing traitor you are! Hands up where I can see them, now!"

Suddenly, a purple flash bomb landed between Shadow and the Agent, blinding them both. Shadow felt two arms wrap tightly around his waist and could hear the beat of two wings softly whistling through the air. Rouge, the now former GUN agent that immediately left the organization after they started a man-hunt for Shadow. She seemed to show up when things were looking their worst.

The bat carried her heavy and tired cargo on top of a high skyscraper. Up here a lot of the heat of the lava below did not reach, and the building seemed stable enough. Plus this building used to house a top-secret Soleanna Government lab. It was shielded from outside signals and contained top-secret information about Soleanna the remaining Heroes found very helpful. Plus all the lava kept humans away, who could not fly on their own.

"Shadow we seriously need to find the Chaos Emeralds again, so I don't have to keep carrying you up to this building! Chaos Control would come in handy for so many things! My back muscles are killing me!"

"The Chaos Emeralds may not be around, but look at this!"

Shadow reached his hand behind his back, and suddenly a beautiful Sky Gem materialized in his hand. Rouge gestured she wanted to touch the beautiful Gem and Shadow handed it to her. The light blue sparkles coming from the rectangular jewel tickled her face.

"Shadow, how did you get it?"

"I didn't. Sonic gave it to me."

"What, why?"

"To try to help me. Sonic found it and showed me he could teleport to wherever it was thrown, a form of Chaos Control! He wanted me to have it to see if I could use full Chaos Control with it… but…"

"But what Shadow?"

"This Sol Emerald is useless to me… that Blue Hedgehog can use a power I cannot!


	2. Chapter 2: Sol Control

Chapter 2: Sol Control

Author note: In response to a review and in fact as you will see in this chapter, I have tweaked the powers of the "Gems." I know very well how the GUN Drive works, but the in-game description claims he teleports to the Gem, so why not? Truthfully, I was going to use the Red Gem earlier and changed it last minute. Plus I of course know about the shoes, but in this version of the story, the shoemaker doesn't exist anymore, kind of sad, huh? Actually, I had a note about this here already, because I make the Green Gem in this chapter much cooler than it actually is, don't you wish the Green Gem did what I say it could do in this chapter?

Soon after Sonic handed the Gem over to Shadow, Sonic ran across an endless stretch of lifeless ground. Once, this used to be Frog Forest. Now the rotting remains of giant mushrooms lay across the ground and gave the area an acrid smell. The bones of giant frogs were an occasional obstacle in Sonic's path. Sonic was getting hungry, he was thinking about going to his base, where cans of food waited for him. But he ran on. He could sense the presence of yet another Sol Emerald here. Since he grabbed one, he now knew what it's energy felt like, similar to the Chaos Emeralds, but different enough where he couldn't "sense" them properly before. Knuckles had always had the ability to sense these Emeralds, but the Flames always got them first. He hoped Shadow appreciated the Gem he gave him and was now happily using Chaos Control like he used to before. A green glimmer half-buried in the ground caught Sonic's eye. This glow reminded him of Amy's eyes. Most of his friends were now gone, he had helplessly watched many of them die as they bravely tried to fight the Flames. But Amy only a month ago just disappeared. Sonic tried to find her for awhile, but gave up. Sonic now was alone, occasionally meeting up with and helping Rouge and Shadow, he was one of their last remaining allies. Sonic knew in his heart people were always afraid of Shadow, even the GUN agency that employed him. They just needed the slightest excuse. But now he knew the new Emeralds could be used too, hope returned to his heart. Sonic bent over and picked up the beautiful Green Sol Emerald.

"Yes!"

Sonic immediately threw the Gem, but nothing happened.

"What's wrong with this one?" said Sonic in a very confused voice.

Angry, Sonic picked it up again, this time spinning around before he was about to throw it. But suddenly he found himself kicking up a violent Tornado. This was much more powerful than his ordinary Tornado move. Soon a spinning blue cyclone was ripping a path through the barren ground. Sonic could only stand there in shock.

"Well, I guess each Sol Emerald does something different!"

--

Back in the Base, Rouge continued to stare at the beautiful Sky Sol Emerald that was in the puzzled Shadow's hand. Rouge thought of the obvious solution.

"Why don't you just say "Sol Control!" That rhymes and everything!"

Shadow gave Rouge a weird look that said "Who cares if it rhymes? And I was about to try that anyway…" Shadow concentrating greatly thought of reappearing next to Rouge.

"Sol Control!"

The hedgehog and bat stared intently at the Emerald, waiting to see if even a flicker of new power would come from the Gem. Nothing. An already weary Shadow just sat the Gem on a nearby table and laid down on the couch, closing his eyes. It was always so boring here, there was nothing to do except clean the place and keep their precious plant collection watered and the light above them on with generator power. That is why he and Rouge were usually out and about, keeping tabs on each other with wrist communicators so Rouge could bring him back.

After 15 minutes had passed, Rouge quietly walked over to the sleeping Shadow. She did this sometimes, and thought his reaction was quite funny and sad at the same time. Rouge rubbed the sleeping hedgehog's shoulders. Still in his sleep he seemed to relax. There was so much tension that would build up in his muscles, she knew doing this when she got the chance would help so much. But of course, she liked massaging Shadow, she just wish he would agree to it when he was awake, or agree to anything else even remotely intimate she even slightly hinted at. If she said anything too strong, he would even turn around and run away like Sonic did from Amy. (Think end of Shadow's story in Sonic Rivals, if you know about it.) But when he was sleeping, she could tell Shadow really liked to be touched, even if he didn't realize it or something. She just couldn't figure this man out.

"Do all male hedgehogs have this strange intimacy problem or something?" she said under her breath as she continued.


	3. Chapter 3: What Happened to Amy

Chapter 3: What Happened to Amy

Sonic was having fun creating violent windstorms, watching frog bones twirl around in the air. "Kind of destructive, but could come in handy" But his thought was interrupted by a familiar sound. Eggman's Eggmobile… Sonic gave that fat old man who was the real cause of everything wrong in everyone's life a death stare. Eggman just sneered back.

"I see you found a Sol Emerald before the creature did! Could you please be so kind as to bring it with you to my base? I want to show you something!"

"Heh, actually it's the second one I have found! I'm just that cool! And are you kidding Eggjerk? Let's see what a nice windstorm would do-"

Sonic stopped in mid-sentence. A white robot appeared beside Eggman holding a capsule that clearly contained Amy!

"I found your little girlfriend a month ago trying to fight the Flame herself. She had third degree burns over seventy percent of her body. But this healing capsule which I used on Shadow after his little fall does wonders, no? She's not completely healed yet, Shadow's much tougher than she and the process is taking quite a while. But if you want her back, I would suggest you hand me the Sol Emerald! I could easily drop her, you know. But truthfully all I am trying to do is help you, but I knew you wouldn't believe me."

Sonic gave Eggman a look of pure evil, then he started to follow Eggman back to his base. He was curious what Eggman was talking about, but now he would of course get to see where Eggman's base was. But Eggman thought of that.

"Sonic, I want you to put on this blindfold, and let one of my robots escort you."

Sonic sneered at Eggman again, but put the blindfold on. After what seemed like hours but was really only 15 minutes, the robot finally put Sonic down. Sonic took the blindfold off his eyes and he could tell he was in a very typical Eggman base. Various machines, robot maintenance, various capsules, etc. Amy's capsule was now situated in the middle of the room. Amy didn't look too bad at all, that capsule at this point had almost restored Amy to her former looks. She looked like she was just resting peacefully, with a few red places here and there. He wondered why Amy had done what she did, he had told her so many times she didn't stand a chance against the Flame on her own.

Eggman pointed to a small metal platform. "Set the Sol Emerald in there, please."

Sonic narrowed his eyes, but did what Eggman said. A small glass shield surrounded the Emerald. Eggman seemed to fiddle with the settings on the device, and a strange blue electric field surrounded the Emerald.

"Watch what happens Sonic when I reverse it's charge!"

The change in field caused an immediate reaction to the Emerald. The green light from the Emerald almost blinded Sonic. Then Eggman switched the machine off. Sonic just stared at the Emerald in amazement. What was once the Green Sol Emerald now looked like the Green Chaos Emerald!

--

Meanwhile back in Shadow's and Rouge's base, Rouge was still rubbing Shadow's back. She almost jumped out of her skin when Shadow very suddenly opened his eyes. She thought she was in trouble! But the truth was Shadow with his super-sharp senses had picked up the sound of an intruder at the door of their base.

"Rouge, grab the Sol Emerald and wait here, I hear something outside."

In fact, Rouge could now hear it too with her sharp bat hearing, she was just too distracted earlier. Shadow was relieved when he saw it was just Omega. Omega was serving as a double agent. He was still working for GUN, but secretly gave information to Rouge and Shadow on the side. Shadow opened the door to the base… only to be shocked when their friend suddenly shot him in the arm!


	4. Chapter 4: Betrayal!

Chapter 4: Betrayal!

Sonic still stared at the beautiful Gem behind the glass shield. Did it just look like a Chaos Emerald now, could it be used like one?

Eggman could see the wonder in his face. "The Sol Emeralds and the Chaos Emeralds are one Sonic. This confirms what I suspected about Eggman Nega, his world is actually one possible version of the Future, when all the Emeralds happened to be Sol Emeralds. Completely releasing the Flame into the world reversed the fields in all the Emeralds and even took away Shadow's ability to use limited Chaos Control without an Emerald. If I can reverse the fields of more Emeralds and-"

Eggman was interrupted when Sonic shockingly spin-dashed into the machine. Sonic knew that this was useful info, but he didn't want Eggman to be the one to have the power of the Chaos Emeralds again. In the past, Sonic had accepted Eggman's help before when the monsters he had released went out-of-control. But this time, Sonic was just too angry. He knew he could get Rouge and Shadow to help reverse the other Emeralds now that he knew how it could be done. Before Eggman could do anything, Sonic had smashed the machine and grabbed the Chaos Emerald. Eggman was outraged.

"I was just trying to help, if we reverse all the Emeralds again and make it so they can't change back, we might be able to stop the Flames! I'm not even trying to catch it now, I just want to stop it! Give me back the Chaos Emerald now, or I'll hurt Amy!"

"Too late Eggman, the Emerald is mine! Chaos Control!"

With that, both Sonic and Amy disappeared from Eggman's base.

--

Rouge and Shadow were in total shock. Shadow was holding the wound on his left arm and was backing away from Omega as small drops of blood fell to the floor. A swarm of GUN Agents soon appeared behind Omega, guns ready to fire. A memory of when those people were happily telling him jokes at an organization picnic flashed into his head.

Shadow had a complete look of shock on his face. "Omega, why did you let them reprogram you?"

"They did not reprogram me Shadow. I saw their point-of-view. You caused this catastrophe, you are too powerful. I can stop you Shadow. Eggman created me to keep you in line. Surrender now, or I will defeat you."

Shadow looked back at Rouge, then looked ahead at Omega. Shadow was thinking about taking off his bracelets, but the soldiers would start firing as soon as he made a gesture like that, plus if he couldn't use Chaos Control, what other powers of his might fail? "Just take me, leave Rouge alone."

"Shadow!" Rouge couldn't believe Shadow was going to give himself up to save her!

Shadow walked slowly up to the GUN agents, and allowed them to handcuff him.

But suddenly… a blinding green light filled the room. Shadow not even knowing what was going on, used the opportunity to kick Omega backwards, making sparks fly in all directions form the robot. Omega and the GUN agents recognized the light as Chaos Control. Knowing what Shadow could do with a Chaos Emerald, Omega and the agents made a hasty retreat back to their helicopter.


	5. Chapter 5: Relocation Plans

Chapter 5: Relocation Plans

Shadow turned around and saw Sonic smirking at him, holding the Green Chaos Emerald. Next to him was the very capsule that Eggman put him in after his fall to Earth, containing Amy.

"Heh, looks like I arrived in time for a party!"

"Where did you find a Chaos Emerald!"

Sonic pointed to the Sol Emerald the still shocked Rouge was holding.

"Eggman turned one of those beauties into one of these beauties by just simply reversing it's magnetic field. And he saved Amy from the Flames. He's might be same ol' Eggman, but he comes in handy sometimes."

Suddenly, the Chaos Emerald started to spark quite wildly. Before their very eyes, the Emerald reverted back to the Sol Emerald shape.

"Hmmm, I guess Eggman's transformation didn't last very long! Anyway, Shadow, how's that Sky Sol working out for you?"

Shadow gave Sonic an angry look.

"Can't use it huh? Well, that doesn't matter, if we can figure out how to reverse the fields in the Emeralds ourselves and keep it permanent we will have the full power of at least two Chaos Emeralds back on our side!"

Rouge looked at Sonic confidently. "I'm sure we can Sonic! But first we need to relocate, since GUN now knows where we are because of that traitor Omega… and I know the perfect place! But first, let's get those handcuffs off Shadow and help his arm."

Rouge was talking about the Aquatic Base lab under the city of Soleanna. She knew of this place because of the records of it in their building, but she discovered only a few weeks ago that a cave on the side an underwater cliff still lead to this place. This place seemed to be shielded from intense heat, created to help contain the Flames if they ever got out and the water surrounding it wasn't enough. Sonic didn't like the description of this place for obvious reasons, but it did contain equipment that would help them. But there was a problem, Amy's capsule was too heavy to carry there.

Rouge using her spy skills removed the handcuffs. While she was cleaning and inspecting the wound on his arm, Shadow looked at the trapped Amy very carefully.

"You know, I think she might be okay enough to release form this thing."

"But Shadow, what if she's still in pain or something, or worse yet she dies?"

"We can always put her back in. Plus I doubt GUN would do anything to harm her if they found her here if we have to leave her behind."

"Well okay Shadow, let's release Amy!"


	6. Chapter 6: Remembering Knuckles

Chapter 6: Remembering Knuckles

Everyone stood in excited anticipation as Rouge typed in the command code on the capsule that would open it. The orange liquid inside drained out slowly and spilled upon the floor. Suddenly, Amy's eyes fluttered open, and with deep breaths she coughed up the highly oxygenated liquid that was filling her lungs. She was very, very disoriented and couldn't figure out where she was or what just happened to her. Her last memory was using her hammer to chuck one last boulder at the beast. This seemed to hurt it some, but then the smoke started to choke her, and everything started to feel so hot… She could feel some pain, but now her vision had become perfectly clear. Her beloved Sonic was standing there. Immediately forgetting everything else around her, she leapt at Sonic, grabbing him tight around the waist, squeezing him hard.

Shadow gave Rouge a look that perfectly conveyed "At least she doesn't rub him in his sleep." Rouge just turned her head away, a slight blush appearing across her cheeks.

"Amy, I can't breathe, and your lack of clothes doesn't help."

"Sorry!" Said Amy in a still happy voice, but then she just sounded confused. "Why am I all wet and in Rouge and Shadow's base? Ahhh! Get me some clothes!"

So Sonic, Rouge and Shadow first handed Amy a t-shirt, it was the best they had. Then they explained to her the crazy events that happened in the span of only a few hours. It was apparent Amy was still bothered by some of the sore-looking spots on her body, but other than she seemed fine.

"Well then, what are we waiting for! Let's move! And make sure to bring your pretty plants too!"

Sonic smiled at Amy's opportunistic and strong personality. If you were to grill Sonic very hard as to what if anything he really liked about Amy, that would be it.

So Rouge, still annoyed she was flying a bunch of people and things around, escorted everyone to the entrance of the base. There was a small part of the water under a rock overhang not on fire, and it was a short underwater swim to get into the cave that lead to the entrance. The crafty bat was easily able to deactivate the base's crazy assortment of security lasers and doors. Sonic literally freaked out when Rouge flew him straight into water! But the bat held his hand and literally pulled him toward the cave. Sonic was glad when his head came above water again and he could get a breath of air. Amy and Shadow had gone before him because they were less scared and were already arranging things and plants in the huge Aquatic Base area.

Rouge smiled "I was thinking about making this our new home anyway Shadow, but seriously, you need to learn to swim also! I'm having back spasms here!"

Sonic had something else on his mind, the Master Emerald. Angel Island used to float serenely above the Flames. To Knuckles' dismay, it had become a refuge camp for many humans and anthros. But only three months ago an anthro named Fang had stupidly grabbed the Master Emerald… sending Angel Island and poor Knuckles and everyone else along with it crashing into the Flames. Sonic had taken back the Master Emerald from the weasel-wolf who stole it and was guarding it himself in his secret base located in the former Sky Canyon area that was high enough to escape much of the flames.

"Hey Rouge, tomorrow don't forget we need to grab the Master Emerald, okay?"

"You want ME to grab the Master Emerald? Imagine what Knuckles reaction would-"

Rouge stopped when she realized she mentioned the name of one who already died and everyone, even Shadow, had a small frown on their face. "Yeah, tomorrow Sonic, but tonight, let's all get some rest."

Everyone was so very weary, and three out of four of them were in physical pain too. The generator lights were dimmed in the underwater base, and everyone found their own warm blanket in separate rooms. Rouge for a little while sat there, watching fish swim by the window. _Lucky fish, they don't have to deal the Flames above. To be a fish, to not have to suffer the way everyone in the above world does. It must be nice._ With that thought, Rouge laid down on her own blanket. She normally hung upside-down and she normally couldn't fall asleep unless it was daylight, but tonight she was just too tired. She fell into a sound sleep.

Suddenly her wings were grabbed, and a hand was placed over her mouth so she could not scream.


	7. Chapter 7: The Attacker Revealed

Chapter 7: The Attacker Revealed

Eggman with a cheesy grin on his face was flying over Sky Canyon. The creepy pumpkin head rock formations with glowing yellow eyes always sent a chill through his spine, especially at night, but he was just overjoyed that he had picked up a signal from the Master Emerald.

"That pesky hedgehog smashed my machine, but at least his Chaos Emerald will revert back to a Sol Emerald soon enough, darn hedgehog didn't even hear me out, I need the Master Emerald to make the change permanent!"

Eggman spotted a small cave by an abandoned rail. Eggman cautiously entered the cave holding a flashlight, not knowing what he would find. He first grabbed some of the cans of unopened food. Canned food is the major currency in this new Flame-ridden world, Rings had very little value anymore. There was a pile of blankets in one corner of the cave, covered with little blue hairs and a few quills here and there. Eggman was leery that two hedgehogs could be nearby, waiting the spin-dash him and wallop him with a huge hammer. But there seemed to be no signs of them to Eggman's relief. Then he caught a faint green light coming from the back of the cave. Eggman grinned widely and cautiously walked closer. The Master Emerald shown in all of it's brilliance, lighting up the small room it was in. It had not changed shape, the Master Emerald had two polarities so it could either neutralize or amplify the Chaos Emeralds and it was still Master of the Sol Emeralds too. With a huge smile, Eggman claimed this beautiful Emerald for himself.

--

Rouge with strong kicks tried to break free from the grip of what she could determine was a very strong anthro man. The way he started stroking her upper back, she was afraid this intruder was about to take advantage of her. But suddenly a very familiar voice said "Heh, now the tables have turned." The hand removed itself from her mouth. Rouge relaxed, a little.

"Shadow, you scared the heck out of me!" said Rouge in a very soft whisper so Sonic and Amy in other rooms would not be disturbed.

"Hmph, how do you think I felt the first time you did this to me? You are just lucky I am not as jumpy as you are and recognized it was you right away."

Rouge didn't know what to say. _I did that at least five times to him, why didn't he bring up he knew earlier? Probably because he liked it and didn't want to admit it._ But she didn't care that much, in that moment. She was starving for a man to touch her. He started to rub the bones in her wings. Her aching wings needed this. _Of course, that is why he is doing this, he just wants to make me feel better because I am his friend, nothing more. Or is there something more on this black hedgehog's mind? Would he? Can he? _She just had to know. Rouge touched her lips to his. She was a little amazed that his lips kissed back, a little.


	8. Chapter 8: Talking about Feelings

Chapter 8: Talking about Feelings

Morning brought with it Amy Rose heating cans of food over a makeshift fire. The smell of corned beef hash woke up the now rested residents of the underwater haven. Shadow and Rouge emerged from the same room and Sonic and Amy looked at them slightly strange, but they didn't really think that much about it. Amy lobbed spoonfuls of the good smelling beef with potatoes into bowls and the others eagerly took them. Rouge looked at Shadow with an obvious blush beaming across her cheeks. Shadow looked at her for a moment, but then went back to shoving spoonfuls of the delicious hash into his mouth. Amy was giving Sonic the look that always make him feel nervous, and he had to look in another direction.

When the food was finished Rouge spoke up "I might as well go get that Master Emerald!"

Sonic nonchalantly said "I'll go with you in case you get into trouble along the way! These Emeralds will come in handy."

Shadow, even with his injured arm said "No, I would rather go Sonic, especially since you wouldn't enjoy taking that little dip through the water again."

Sonic wondered why Rouge suddenly looked at Shadow so strangely, but then she just started walking off to the entrance of the layer, with Shadow following close behind.

As soon as they left, Sonic realized he was trapped in an underwater base with Amy. Throughout this entire deal, if Amy got a little too clingy, he could always run around for a while. Sonic turned around, and sure enough Amy was standing there with that look in her eye. But what she said didn't really surprise him, but still caught him off-guard.

"Sonic, how did you feel when I was gone?"

Sonic stood there for a minute, but then sat down at a nearby table. Sonic gestured he wanted Amy to sit down in the chair next to him. She gladly accepted the offer. She was taken aback when Sonic stared directly into her eyes.

"I looked for you of course! What else do you think I would do Amy?"

"Well, I figure that, but I asked how you felt, not what you did!"

"Well, um… I, I don't know, but why did you do what you did Amy?"

"Because of Tails, and Knuckles and everyone else! Before the Flame got Tails, he was making progress! Those Ring Bombs were doing some damage to the creature! Maybe if it was damaged enough, it would give up an Emerald! I was helping him by hitting rocks at it too with my hammer, but then it got him. Tails! I couldn't believe how you reacted! It had to be punished for what it did to Tails! You, Sonic, you did nothing. You were afraid." Amy walked off to another corner of the base. Sonic just sat there and put his head between his hands. What she had said was mostly true. But he was not afraid, just horribly guilty and discouraged.

--

Rouge while carrying Shadow thorough the air didn't know what to say, if anything for quite a while. He must have wanted to talk, but why didn't he say anything? The perfect question popped into her head.

"Shadow, how did you feel last night?"

"Nothing!"

"Don't lie to me Shadow! You have as many feelings as anyone else!"

"Damn it, I don't know! Okay?."


	9. Chapter 9: Master Emerald Caused Worry

Chapter 9: Master Emerald Caused Worry

Rouge didn't know what to say, they were almost at their destination anyway_ I don't know? Does he not love me? Or was it a feeling he never felt before, so he is confused about it? _Rouge sat Shadow down at the entrance to the dark cave. Shadow looked at Rouge like he was going to explain what he just said, but then decided to say nothing. When Rouge and Shadow shown their light into the cave, they could immediately tell the cave had been ransacked. Nothing of value had remained, most importantly the Master Emerald.

Shadow stomped his foot. "Damn it!"

Rouge looked angry. "Oh great, now what are we going to tell Sonic, hmm?"

Shadow seemed to be calming down, some. "I bet twenty cans of food Dr. Eggman took it!"

"But Shadow, we don't know where Eggman's base is! Let's just go back and tell Sonic, he's more powerful than you are now anyways since he can use the Sol Emeralds!"

Shadow just sneered at Rouge with a look that perfectly said "Thanks for reminding me!"

Rouge felt sorry, so she went up to him and patted him on the back. "I'm sorry Shadow. But there is one thing I need to know, why don't you know how you felt about last night? I'll tell you I liked it, and I think that we should do it again sometime, hmm?"

"Damn it woman stop petting me! We have more important things to worry about now!"

The two headed back to Aquatic Base, not saying another word to each other.

--

Eggman's grin turned into a frown at the info on his console. The Master Emerald's power proved to be a great tracker. He could clearly see the Creature had absorbed the power of four Sol Emeralds. Two were mysteriously under the City of Soleanna, Eggman assumed these where the ones Sonic was bragging about finding, he really liked having this info handy. And one was smack dab in the middle of the Oil Ocean Zone. The Flames had almost reached the end of this very flammable Zone, and he knew the creature's power would increase dramatically with the energy from that fifth Emerald.

Eggman immediately took out a communicator and pressed a button on it.

--

A very defeated looking Rouge walked into the base with an angry looking Shadow.

"I'm sorry Sonic, the Master Emerald and your food was stolen by someone."

"Eggman! But I don't know where his base is, but I've been there so I think Chaos Control would be possible! Rouge and Shadow, do you think one of these machines in here could reverse the field of these Emeralds, even briefly?"

Rouge looked over at one machine, which she didn't know used to be part of the device that contained the Flame. "I think this one generates electromagnetic pulses, if I can set it just right…"

Rouge knew this was probably crude based upon what Eggman did, but she took a reading from the Sol Emeralds, and set the device exactly opposite to it in charge and at the same strength. Applying the field, the Emeralds briefly changed shape, but quickly reverted back to Sol Emerald.

"Hopefully we don't have to use their power too long. Maybe the effect would last longer if field was stronger and it is exposed to the energy longer, to allow more of the Emerald's molecules to line up with-"

Rouge looked at him "You don't have to explain it Shadow, just do it!"

The four heroes just stood there, staring at the Emeralds while Shadow charged them up for a good 15 minutes. After that period of time, the Emeralds seemed as Chaos as ever. Sonic grabbed both Emeralds, but then Shadow took the Green one from him. The Green one had always been Shadow's favorite, since it was Shadow's first Chaos Emerald and the one he used the most. He seemed to smile when he could feel his old power seep into his soul once again from the Emerald he often thought of as "his" .

"Let me do this Sonic! You should be able to still guide where we end up!"

Shadow yelled "Chaos Control!" at the top of his lungs, teleporting both him and Sonic to Eggman's base.

If only Shadow had figured out at that point in time how to properly use two Chaos Emeralds and two people who could use Chaos Control, then maybe they could have changed the past then and there, before it was too late.


	10. Chapter 10: Shadow the Liar?

Chapter 10: Shadow the Liar?

Only two minutes after Shadow and Sonic disappeared, Rouge and Amy heard loud banging coming from the entrance to their base.

"Rouge, someone has found us!"

Amy got out her trusty Piko Piko while Rouge was preparing her bombs and her feet. A clunking sound was coming down the hallway. Rouge recognized that sound anywhere, it was Omega.

"Where is Shadow? Give him up now."

"He is not here Omega! And anyway he is our friend, remember and I am your friend too! We fought so many battles side-by-side, how could you do this? It's not fair!"

"I have seen evidence you have not. I saw a video which clearly depicted Shadow at the crash site. This video was from an official source. He was trying to kill the Princess because he found out about the Flames and sabotaged Eggman's Battleship. Shadow was programmed by Gerald to destroy the world after Gerald went insane. Shadow could not overcome his programming, that is why he must be stopped. He is not our friend. He has been lying to you. It would have been better if you did not know this information, but now you do."

Rouge became hysterical. _Maybe he said what he said because he really didn't love me, he was lying to me. And he used me. No, that't can't be right! I feel it in my heart! _ "No! That's not true! It can't be true! It was Sonic, not Shadow they saw, and he was trying to save the princess! It's not true Omega!"

--

Eggman was still wondering if he should bother getting that Emerald in the Oil Ocean Zone before the creature did. It would have been nice, but the creature was too close and he didn't want to find himself in the middle of a burning oil field. Suddenly it seemed the entire room was lit up with a bright green light. Eggman turned around and was faced with two hedgehogs staring him down, holding two Chaos Emeralds. Eggman picked up the communicator, and said something into it very quietly, then turned to the hedgehogs.

"So, figured out my little transformation trick for yourself, huh? What do you want?"

Sonic was feeling very confident now. "I want the Master Emerald back, now!"

"You do, huh? I have already used it to find where the other Sol Emeralds are located. In fact, if we don't retrieve one of them very soon, the Flames will get yet another one, so you have greater things to worry about!"

"Do you think this is funny Eggman? I don't believe one word that comes out of your mouth! I'm taking back the Master Emerald, now!"

With that, Sonic and Shadow easily grabbed the Master Emerald… a bit too easily, then they used Chaos Control again right back to their base, while Eggman was talking to his communicator again.


	11. Chapter 11: The One Who Defeated Shadow

Chapter 11: The One Who Defeated and Sealed Shadow

Sonic and Shadow teleported right into a trap. Eggman had quickly told Omega they were about to Chaos Control back to the base, and he was now ready for them to appear. Before Shadow even had the chance to defend himself, shots rang out from the robots' arms.

Most of the rounds hit Shadow. The stricken dark hedgehog looked into Rouge eyes and said "Damn it! This will not defeat me!" before collapsing on the ground in a thick pool of dark blood. One round had lodged itself into Sonic's side, the blue hedgehog was now laying in another small pool of bright blood with no signs of movement.

Amy let out a blood curdling scream and immediately ran to Sonic, and Rouge just looked at Omega, with tears in her eyes. Rouge was about to throw every single bomb she had at Omega, but Omega was now pointing his arms at her, and she knew it was best to just back off. She and Amy didn't have enough power to stop him, and the Emeralds were useless since Shadow and Sonic were possibly dead.

"How dare you Omega, how dare you! You didn't even give Shadow a chance to fight back! How did you find us anyway?"

"Dr. Eggman saw the signals from the Emeralds and tracked down where you were. Then he told me they were using Chaos Control and would most likely return here."

"Now Dr. Eggman is on your side? Was he the one that reprogrammed you?"

"No one reprogrammed me. Hand over Shadow and the Emeralds, and I will spare the rest of you."

Sparks distracted Rouge and Amy for a second, as the two Chaos Emeralds seemed to be changing back to Sol state. But then the Master Emerald sent out an electric arc, they remained Chaos Emeralds. The Sky and Green Emeralds we now shielded from the transformation effects of Iblis, which is why they remained unchanged long into the future.

Rouge started to cry. "_Omega's wrong! I don't care what stupid video he saw!"_

"Even if you believed that Shadow was the enemy, you didn't even give him a chance to fight back! You choose to shoot him down in cold blood! He was willing to give himself up to save me earlier, it's what Shadow would have done. Go ahead, take him Omega. And feel guilty for what you have done, if robots can feel guilt that is."

"You can keep the Emeralds." said Omega in his normal mono-toned voice. Rouge cried as she watched Omega leave with a very bloody Shadow draped across one shoulder. She felt her heart was ripping in two. _I will rescue you someday!_

Omega was taking him to a secure GUN facility, to be sealed away forever in a special machine so he could never escape. They feared the Ultimate Life Form could recover from even fatal-looking wounds.

When the robot was gone, a small sound came from Sonic and Amy gasped. His emerald eyes opened and he clutched at the painful wound in his side. Amy patted the top of his head. "It's going to be okay Sonic. You'll get Shadow back when you get better, right?"

"Of course I will Amy."

A sickening rumbling could be heard somewhere in the distance. They hated that sound, it meant the Flames had claimed another Sol Emerald. More people would die and more devastation would come to their world. Amy just looked up, with the most determined face she ever wore.

"Some day, those Flames will be defeated, if not by us then by our descendents!"

--

A few hours later, Eggman calmly walked up to GUN headquarters. Not many GUN soldiers where there, they were all off trying to evacuate more people from the fast spreading Flames. But the Commander in charge was there. Eggman found it hard not to stare into the Commanders' odd eyes. He didn't want to this time, there was something about this eyes Eggman didn't like, beyond the outward unusualness that they were two different colors.

"I have kept my end of the bargain, now for you to keep yours! The Emeralds, please."

"Heh, we didn't recover the Emeralds, and even if we did, do you think we would have really sided with you?"

"But, you don't know how to change the Emeralds back! I know how to stop the Flames, it's not fair!"

"But it is fair, since you were a tool all this time so I could have what I wanted, which I now have. I caused your battleship to malfunction. And I framed Shadow by editing the video tape of Sonic at the crash site and I spread the rumors he released the Flames."

"YOU released the Flames? Why?"

"I got what I wanted, GUN and the President against Shadow, and Shadow finally locked up for what he did to Maria and everyone I loved 50 Years Ago!"

"How dare you! I will tell the world what you did!"

"Guards, arrest him!"

As the guards cuffed Eggman, the Commander smiled while twirling the unbroken Scepter of Darkness around gleefully.

The End

But there will almost certainly be a sequel…

Note- I'm assuming that breaking the Scepter is what caused the Time Line changes in Sonic 06 and was a Time Paradox, in this story like in Kitty Cat Crisis, Shadow caught the Scepter instead of Rouge when it fell and handed it to GUN as ordered.


End file.
